Casal2 Test Case MPD comparisons for BCO

1 BCO comparison of CASAL and Casal2 model configurations

This document compares the results of at least 2 CASAL model configurations (base and at least one sensitivity) and up to 6 Casal2 model configurations (3 BetaDiff and 3 ADOL-C).

The CASAL model sensitivity 1 has a smaller minimisation tolerance value than the CASAL base model (1e-7 vs. 2e-5).

The Casal2 ADOL-C and BetaDiff low tolerance models have a smaller tolerance value than the CASAL base model (1e-7 vs. 2e-5).

1.1 BCO model characteristics

The main characteristics of the Test Case BCO (ling) CASAL model are:

• one stock, ages 3 - 20
• one area
• years 1900 - 2019, projection year 2020
• one time step
• two stock categories: male and female
• natural mortality-at-age is 0.14 for males and 0.20 for females
• sex-specific logistic maturity
• sex-specific von Bertalanffy age-length relationship
• one length-weight relationship (\(W = aL^b\))
• Beverton-Holt stock-recruitment relationship, with steepness (h) 0.75 and \(\sigma_R\) 0.6
• no ageing error
• one survey with sex-specific age-based logistic selectivity
• three fisheries, all with sex-specific length-based logistic selectivity and retained/discarded catches

Observation data include:

• survey index
• fishery CPUE index
• fishery proportions-at-length

Parameters estimated include:

• B0
• male \(L_{\infty}\)
• male age-length CV2
• sex-specific survey logistic selectivity (a50 and ato95)
• YCS (recruitment deviations)

1.2 R environment

## [1] "Fri Sep  9 12:43:57 2022"
## R version 3.6.0 (2019-04-26)
## Platform: x86_64-redhat-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
## 
## Matrix products: default
## BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
## 
## locale:
##  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
##  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
##  [7] LC_PAPER=en_GB.UTF_8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] Casal2_22.09   casal_2.30     devtools_2.4.4 usethis_2.1.6  rlist_0.4.6.2 
##  [6] ggthemes_4.2.4 gridExtra_2.3  coda_0.19-4    ggmcmc_1.5.1.1 ggplot2_3.3.6 
## [11] tidyr_1.2.1    huxtable_5.5.0 dplyr_1.0.10   plyr_1.8.7    
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.9         lattice_0.20-38    prettyunits_1.1.1  ps_1.7.1          
##  [5] assertthat_0.2.1   digest_0.6.29      utf8_1.2.2         mime_0.12         
##  [9] R6_2.5.1           evaluate_0.16      pillar_1.8.1       rlang_1.0.5       
## [13] data.table_1.14.2  miniUI_0.1.1.1     urlchecker_1.0.1   callr_3.7.2       
## [17] jquerylib_0.1.4    rmarkdown_2.16     stringr_1.4.1      htmlwidgets_1.5.4 
## [21] munsell_0.5.0      shiny_1.7.2        compiler_3.6.0     httpuv_1.6.6      
## [25] xfun_0.32          pkgconfig_2.0.3    pkgbuild_1.3.1     htmltools_0.5.3   
## [29] tidyselect_1.1.2   tibble_3.1.8       reshape_0.8.9      fansi_1.0.3       
## [33] crayon_1.5.1       withr_2.5.0        later_1.3.0        grid_3.6.0        
## [37] jsonlite_1.8.0     xtable_1.8-4       GGally_2.1.2       gtable_0.3.1      
## [41] lifecycle_1.0.1    magrittr_2.0.3     scales_1.2.1       cli_3.4.0         
## [45] stringi_1.7.8      cachem_1.0.6       remotes_2.4.2      fs_1.5.2          
## [49] promises_1.2.0.1   bslib_0.4.0        ellipsis_0.3.2     generics_0.1.3    
## [53] vctrs_0.4.1        RColorBrewer_1.1-3 tools_3.6.0        glue_1.6.2        
## [57] purrr_0.3.4        pkgload_1.3.0      processx_3.7.0     fastmap_1.1.0     
## [61] yaml_2.3.5         colorspace_2.0-3   sessioninfo_1.2.2  memoise_2.0.1     
## [65] knitr_1.40         profvis_0.3.7      sass_0.4.2

1.3 CASAL and Casal2 model output

source('../../R-functions/report_read_in_CASAL_MPD_files.R')

source('../../R-functions/report_read_in_Casal2_MPD_files.R')

1.4 Tables

Tables of parameter estimates and objective function components for the CASAL and Casal2 model MPD results

CASAL parameter estimates

rownames	Base_Model	Sensitivity_1	Percent_Diff
initialization.B0	14170.00000	14170.00000	0.000
recruitment.YCS1	1.00000	1.00000	0.000
recruitment.YCS2	1.00000	1.00000	0.000
recruitment.YCS3	1.00000	1.00000	0.000
recruitment.YCS4	1.00000	1.00000	0.000
recruitment.YCS5	1.00000	1.00000	0.000
recruitment.YCS6	1.00000	1.00000	0.000
recruitment.YCS7	1.00000	1.00000	0.000
recruitment.YCS8	1.00000	1.00000	0.000
recruitment.YCS9	1.00000	1.00000	0.000
recruitment.YCS10	1.00000	1.00000	0.000
recruitment.YCS11	1.00000	1.00000	0.000
recruitment.YCS12	1.00000	1.00000	0.000
recruitment.YCS13	1.00000	1.00000	0.000
recruitment.YCS14	1.00000	1.00000	0.000
recruitment.YCS15	1.00000	1.00000	0.000
recruitment.YCS16	1.00000	1.00000	0.000
recruitment.YCS17	1.00000	1.00000	0.000
recruitment.YCS18	1.00000	1.00000	0.000
recruitment.YCS19	1.00000	1.00000	0.000
recruitment.YCS20	1.00000	1.00000	0.000
recruitment.YCS21	1.00000	1.00000	0.000
recruitment.YCS22	1.00000	1.00000	0.000
recruitment.YCS23	1.00000	1.00000	0.000
recruitment.YCS24	1.00000	1.00000	0.000
recruitment.YCS25	1.00000	1.00000	0.000
recruitment.YCS26	1.00000	1.00000	0.000
recruitment.YCS27	1.00000	1.00000	0.000
recruitment.YCS28	1.00000	1.00000	0.000
recruitment.YCS29	1.00000	1.00000	0.000
recruitment.YCS30	1.00000	1.00000	0.000
recruitment.YCS31	1.00000	1.00000	0.000
recruitment.YCS32	1.00000	1.00000	0.000
recruitment.YCS33	1.00000	1.00000	0.000
recruitment.YCS34	1.00000	1.00000	0.000
recruitment.YCS35	1.00000	1.00000	0.000
recruitment.YCS36	1.00000	1.00000	0.000
recruitment.YCS37	1.00000	1.00000	0.000
recruitment.YCS38	1.00000	1.00000	0.000
recruitment.YCS39	1.00000	1.00000	0.000
recruitment.YCS40	1.00000	1.00000	0.000
recruitment.YCS41	1.00000	1.00000	0.000
recruitment.YCS42	1.00000	1.00000	0.000
recruitment.YCS43	1.00000	1.00000	0.000
recruitment.YCS44	1.00000	1.00000	0.000
recruitment.YCS45	1.00000	1.00000	0.000
recruitment.YCS46	1.00000	1.00000	0.000
recruitment.YCS47	1.00000	1.00000	0.000
recruitment.YCS48	1.00000	1.00000	0.000
recruitment.YCS49	1.00000	1.00000	0.000
recruitment.YCS50	1.00000	1.00000	0.000
recruitment.YCS51	1.00000	1.00000	0.000
recruitment.YCS52	1.00000	1.00000	0.000
recruitment.YCS53	1.00000	1.00000	0.000
recruitment.YCS54	1.00000	1.00000	0.000
recruitment.YCS55	1.00000	1.00000	0.000
recruitment.YCS56	1.00000	1.00000	0.000
recruitment.YCS57	1.00000	1.00000	0.000
recruitment.YCS58	1.00000	1.00000	0.000
recruitment.YCS59	1.00000	1.00000	0.000
recruitment.YCS60	1.00000	1.00000	0.000
recruitment.YCS61	1.00000	1.00000	0.000
recruitment.YCS62	1.00000	1.00000	0.000
recruitment.YCS63	1.00000	1.00000	0.000
recruitment.YCS64	1.00000	1.00000	0.000
recruitment.YCS65	1.00000	1.00000	0.000
recruitment.YCS66	1.00000	1.00000	0.000
recruitment.YCS67	1.00000	1.00000	0.000
recruitment.YCS68	1.00000	1.00000	0.000
recruitment.YCS69	1.00000	1.00000	0.000
recruitment.YCS70	1.00000	1.00000	0.000
recruitment.YCS71	1.00000	1.00000	0.000
recruitment.YCS72	1.00000	1.00000	0.000
recruitment.YCS73	1.00000	1.00000	0.000
recruitment.YCS74	1.00000	1.00000	0.000
recruitment.YCS75	1.00000	1.00000	0.000
recruitment.YCS76	1.00000	1.00000	0.000
recruitment.YCS77	1.00000	1.00000	0.000
recruitment.YCS78	1.00000	1.00000	0.000
recruitment.YCS79	1.00000	1.00000	0.000
recruitment.YCS80	1.00000	1.00000	0.000
recruitment.YCS81	1.00000	1.00000	0.000
recruitment.YCS82	1.00000	1.00000	0.000
recruitment.YCS83	1.00000	1.00000	0.000
recruitment.YCS84	0.23480	0.23480	0.000
recruitment.YCS85	0.23160	0.23160	0.000
recruitment.YCS86	0.23220	0.23220	0.000
recruitment.YCS87	0.24120	0.24120	0.000
recruitment.YCS88	0.26510	0.26510	0.000
recruitment.YCS89	0.31720	0.31720	0.000
recruitment.YCS90	0.42240	0.42240	0.000
recruitment.YCS91	0.61390	0.61390	0.000
recruitment.YCS92	0.92300	0.92300	0.000
recruitment.YCS93	1.42900	1.42900	0.000
recruitment.YCS94	1.48000	1.48000	0.000
recruitment.YCS95	1.00900	1.00900	0.000
recruitment.YCS96	0.84620	0.84620	0.000
recruitment.YCS97	0.85550	0.85550	0.000
recruitment.YCS98	1.08700	1.08700	0.000
recruitment.YCS99	1.53000	1.53000	0.000
recruitment.YCS100	1.02700	1.02700	0.000
recruitment.YCS101	0.79990	0.79990	0.000
recruitment.YCS102	0.82080	0.82080	0.000
recruitment.YCS103	0.63180	0.63180	0.000
recruitment.YCS104	0.80520	0.80520	0.000
recruitment.YCS105	0.74530	0.74530	0.000
recruitment.YCS106	0.46340	0.46340	0.000
recruitment.YCS107	1.07500	1.07500	0.000
recruitment.YCS108	0.89920	0.89920	0.000
recruitment.YCS109	0.38510	0.38510	0.000
recruitment.YCS110	0.91270	0.91270	0.000
recruitment.YCS111	0.70920	0.70920	0.000
recruitment.YCS112	0.82900	0.82900	0.000
recruitment.YCS113	0.42330	0.42330	0.000
recruitment.YCS114	1.27800	1.27800	0.000
recruitment.YCS115	0.68810	0.68810	0.000
recruitment.YCS116	0.74250	0.74250	0.000
recruitment.YCS117	0.57050	0.57050	0.000
recruitment.YCS118	0.45160	0.45160	0.000
recruitment.YCS119	1.00000	1.00000	0.000
recruitment.YCS120	1.00000	1.00000	0.000
size_at_age.Linf_male	47.12000	47.12000	0.000
size_at_age.cv2_male	0.06256	0.06256	0.000
selectivity[potSsel].male1	3.03900	3.03900	0.000
selectivity[potSsel].male2	0.19070	0.19060	0.052
selectivity[potSsel].female1	3.31600	3.31600	0.000
selectivity[potSsel].female2	1.04500	1.04500	0.000

Casal2 parameter estimates

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
process[Recruitment].b0	14561.20000	14564.90000	14561.20000	14561.20000	14564.90000	14561.20000
age_length[asMm0].linf	46.77840	46.76270	46.77840	46.77840	46.76270	46.77840
age_length[asMm0].cv_last	0.10000	0.10000	0.10000	0.10000	0.10000	0.10000
selectivity[potSurveySel_male].a50	3.03766	3.03845	3.03765	3.03766	3.03845	3.03765
selectivity[potSurveySel_male].ato95	0.19125	0.19192	0.19124	0.19125	0.19192	0.19124
selectivity[potSurveySel_female].a50	3.30703	3.30808	3.30703	3.30703	3.30808	3.30703
selectivity[potSurveySel_female].ato95	1.03761	1.03043	1.03761	1.03761	1.03043	1.03761
process[Recruitment].recruitment_multipliers{1983}	0.23462	0.23448	0.23462	0.23462	0.23448	0.23462
process[Recruitment].recruitment_multipliers{1984}	0.23232	0.23218	0.23232	0.23232	0.23218	0.23232
process[Recruitment].recruitment_multipliers{1985}	0.23441	0.23428	0.23441	0.23441	0.23428	0.23441
process[Recruitment].recruitment_multipliers{1986}	0.24436	0.24425	0.24436	0.24436	0.24425	0.24436
process[Recruitment].recruitment_multipliers{1987}	0.26857	0.26849	0.26857	0.26857	0.26849	0.26857
process[Recruitment].recruitment_multipliers{1988}	0.32084	0.32085	0.32084	0.32084	0.32085	0.32084
process[Recruitment].recruitment_multipliers{1989}	0.42475	0.42490	0.42475	0.42475	0.42490	0.42475
process[Recruitment].recruitment_multipliers{1990}	0.61282	0.61316	0.61282	0.61282	0.61316	0.61282
process[Recruitment].recruitment_multipliers{1991}	0.91566	0.91626	0.91566	0.91566	0.91626	0.91566
process[Recruitment].recruitment_multipliers{1992}	1.41810	1.41981	1.41812	1.41810	1.41981	1.41812
process[Recruitment].recruitment_multipliers{1993}	1.51893	1.51716	1.51890	1.51893	1.51716	1.51890
process[Recruitment].recruitment_multipliers{1994}	1.01275	1.01199	1.01275	1.01275	1.01199	1.01275
process[Recruitment].recruitment_multipliers{1995}	0.84577	0.84550	0.84577	0.84577	0.84550	0.84577
process[Recruitment].recruitment_multipliers{1996}	0.85847	0.85864	0.85846	0.85847	0.85864	0.85846
process[Recruitment].recruitment_multipliers{1997}	1.09380	1.09463	1.09380	1.09380	1.09463	1.09380
process[Recruitment].recruitment_multipliers{1998}	1.49230	1.49154	1.49228	1.49230	1.49154	1.49228
process[Recruitment].recruitment_multipliers{1999}	1.02713	1.02664	1.02713	1.02713	1.02664	1.02713
process[Recruitment].recruitment_multipliers{2000}	0.79475	0.79461	0.79476	0.79475	0.79461	0.79476
process[Recruitment].recruitment_multipliers{2001}	0.81779	0.81836	0.81779	0.81779	0.81836	0.81779
process[Recruitment].recruitment_multipliers{2002}	0.63458	0.63528	0.63458	0.63458	0.63528	0.63458
process[Recruitment].recruitment_multipliers{2003}	0.81338	0.81405	0.81338	0.81338	0.81405	0.81338
process[Recruitment].recruitment_multipliers{2004}	0.74780	0.74816	0.74780	0.74780	0.74816	0.74780
process[Recruitment].recruitment_multipliers{2005}	0.45632	0.45629	0.45632	0.45632	0.45629	0.45632
process[Recruitment].recruitment_multipliers{2006}	1.03192	1.02929	1.03192	1.03192	1.02929	1.03192
process[Recruitment].recruitment_multipliers{2007}	0.87650	0.87258	0.87649	0.87650	0.87258	0.87649
process[Recruitment].recruitment_multipliers{2008}	0.37796	0.37623	0.37796	0.37796	0.37623	0.37796
process[Recruitment].recruitment_multipliers{2009}	0.90988	0.90567	0.90988	0.90988	0.90567	0.90988
process[Recruitment].recruitment_multipliers{2010}	0.69749	0.70936	0.69749	0.69749	0.70936	0.69749
process[Recruitment].recruitment_multipliers{2011}	0.82770	0.82700	0.82770	0.82770	0.82700	0.82770
process[Recruitment].recruitment_multipliers{2012}	0.42538	0.42510	0.42538	0.42538	0.42510	0.42538
process[Recruitment].recruitment_multipliers{2013}	1.29262	1.29179	1.29262	1.29262	1.29179	1.29262
process[Recruitment].recruitment_multipliers{2014}	0.69582	0.69641	0.69582	0.69582	0.69641	0.69582
process[Recruitment].recruitment_multipliers{2015}	0.75531	0.75529	0.75531	0.75531	0.75529	0.75531
process[Recruitment].recruitment_multipliers{2016}	0.58135	0.58150	0.58135	0.58135	0.58150	0.58135
process[Recruitment].recruitment_multipliers{2017}	0.45244	0.45226	0.45244	0.45244	0.45226	0.45244

Casal2 parameter estimates: Percent Difference from betadiff_casal_flags_on

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
process[Recruitment].b0	0.000	-0.025	0.000	0.000	-0.025	0.000
age_length[asMm0].linf	0.000	0.034	0.000	0.000	0.034	0.000
age_length[asMm0].cv_last	0.000	0.000	0.000	0.000	0.000	0.000
selectivity[potSurveySel_male].a50	0.000	-0.026	0.000	0.000	-0.026	0.000
selectivity[potSurveySel_male].ato95	0.000	-0.350	0.007	0.000	-0.350	0.007
selectivity[potSurveySel_female].a50	0.000	-0.032	0.000	0.000	-0.032	0.000
selectivity[potSurveySel_female].ato95	0.000	0.692	0.000	0.000	0.692	0.000
process[Recruitment].recruitment_multipliers{1983}	0.000	0.064	0.000	0.000	0.064	0.000
process[Recruitment].recruitment_multipliers{1984}	0.000	0.061	0.000	0.000	0.061	0.000
process[Recruitment].recruitment_multipliers{1985}	0.000	0.057	0.000	0.000	0.057	0.000
process[Recruitment].recruitment_multipliers{1986}	0.000	0.047	0.000	0.000	0.047	0.000
process[Recruitment].recruitment_multipliers{1987}	0.000	0.027	0.000	0.000	0.027	0.000
process[Recruitment].recruitment_multipliers{1988}	0.000	-0.003	0.000	0.000	-0.003	0.000
process[Recruitment].recruitment_multipliers{1989}	0.000	-0.035	-0.000	0.000	-0.035	-0.000
process[Recruitment].recruitment_multipliers{1990}	0.000	-0.056	0.000	0.000	-0.056	0.000
process[Recruitment].recruitment_multipliers{1991}	0.000	-0.065	0.001	0.000	-0.065	0.001
process[Recruitment].recruitment_multipliers{1992}	0.000	-0.121	-0.001	0.000	-0.121	-0.001
process[Recruitment].recruitment_multipliers{1993}	0.000	0.117	0.002	0.000	0.117	0.002
process[Recruitment].recruitment_multipliers{1994}	0.000	0.075	0.000	0.000	0.075	0.000
process[Recruitment].recruitment_multipliers{1995}	0.000	0.031	-0.000	0.000	0.031	-0.000
process[Recruitment].recruitment_multipliers{1996}	0.000	-0.021	0.000	0.000	-0.021	0.000
process[Recruitment].recruitment_multipliers{1997}	0.000	-0.076	0.000	0.000	-0.076	0.000
process[Recruitment].recruitment_multipliers{1998}	0.000	0.051	0.001	0.000	0.051	0.001
process[Recruitment].recruitment_multipliers{1999}	0.000	0.048	0.000	0.000	0.048	0.000
process[Recruitment].recruitment_multipliers{2000}	0.000	0.018	-0.001	0.000	0.018	-0.001
process[Recruitment].recruitment_multipliers{2001}	0.000	-0.069	0.000	0.000	-0.069	0.000
process[Recruitment].recruitment_multipliers{2002}	0.000	-0.110	0.000	0.000	-0.110	0.000
process[Recruitment].recruitment_multipliers{2003}	0.000	-0.082	0.000	0.000	-0.082	0.000
process[Recruitment].recruitment_multipliers{2004}	0.000	-0.047	0.000	0.000	-0.047	0.000
process[Recruitment].recruitment_multipliers{2005}	0.000	0.007	0.000	0.000	0.007	0.000
process[Recruitment].recruitment_multipliers{2006}	0.000	0.255	0.000	0.000	0.255	0.000
process[Recruitment].recruitment_multipliers{2007}	0.000	0.447	0.000	0.000	0.447	0.000
process[Recruitment].recruitment_multipliers{2008}	0.000	0.460	0.000	0.000	0.460	0.000
process[Recruitment].recruitment_multipliers{2009}	0.000	0.463	0.000	0.000	0.463	0.000
process[Recruitment].recruitment_multipliers{2010}	0.000	-1.702	0.000	0.000	-1.702	0.000
process[Recruitment].recruitment_multipliers{2011}	0.000	0.084	0.000	0.000	0.084	0.000
process[Recruitment].recruitment_multipliers{2012}	0.000	0.065	0.000	0.000	0.065	0.000
process[Recruitment].recruitment_multipliers{2013}	0.000	0.064	0.000	0.000	0.064	0.000
process[Recruitment].recruitment_multipliers{2014}	0.000	-0.085	0.000	0.000	-0.085	0.000
process[Recruitment].recruitment_multipliers{2015}	0.000	0.002	0.000	0.000	0.002	0.000
process[Recruitment].recruitment_multipliers{2016}	0.000	-0.024	0.000	0.000	-0.024	0.000
process[Recruitment].recruitment_multipliers{2017}	0.000	0.041	0.000	0.000	0.041	0.000

CASAL objective function component values

Component	Base_Model	Sensitivity_1
potCPUE	-51.180	-51.180
potSurveyAbd	-3.254	-3.254
logbookLF	54.660	54.660
potCommAF	54.410	54.410
potSurveyAF	118.200	118.200
recCatchLF	68.040	68.040
prior_on_initialization.B0	9.559	9.559
prior_on_recruitment.YCS	9.658	9.658
prior_on_size_at_age.Linf_male	0.000	0.000
prior_on_size_at_age.cv2_male	0.000	0.000
prior_on_selectivity[potSsel].male	0.000	0.000
prior_on_selectivity[potSsel].female	0.000	0.000
prior_on_q_qPotCPUE	-8.331	-8.331
prior_on_q_potSurveyq	-11.380	-11.380
clp1F	0.000	0.000
clp2F	0.000	0.000
clp3F	0.000	0.000
YCS	0.566	0.566
Total	241.000	241.000

Casal2 objective function component values

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
observation->potSurvey->2010	-1.080	-1.083	-1.080	-1.080	-1.083	-1.080
observation->potSurvey->2014	-1.015	-1.017	-1.015	-1.015	-1.017	-1.015
observation->potSurvey->2018	-1.214	-1.215	-1.214	-1.214	-1.215	-1.214
observation->potCPUE->1990	-0.185	-0.180	-0.185	-0.185	-0.180	-0.185
observation->potCPUE->1991	1.149	1.154	1.149	1.149	1.154	1.149
observation->potCPUE->1992	-0.988	-0.986	-0.988	-0.988	-0.986	-0.988
observation->potCPUE->1993	-1.963	-1.963	-1.963	-1.963	-1.963	-1.963
observation->potCPUE->1994	-2.136	-2.136	-2.136	-2.136	-2.136	-2.136
observation->potCPUE->1995	-2.090	-2.090	-2.090	-2.090	-2.090	-2.090
observation->potCPUE->1996	-2.182	-2.182	-2.182	-2.182	-2.182	-2.182
observation->potCPUE->1997	-1.944	-1.945	-1.944	-1.944	-1.945	-1.944
observation->potCPUE->1998	-2.157	-2.157	-2.157	-2.157	-2.157	-2.157
observation->potCPUE->1999	-1.670	-1.670	-1.670	-1.670	-1.670	-1.670
observation->potCPUE->2000	-2.191	-2.191	-2.191	-2.191	-2.191	-2.191
observation->potCPUE->2001	-2.158	-2.158	-2.158	-2.158	-2.158	-2.158
observation->potCPUE->2002	-2.022	-2.022	-2.022	-2.022	-2.022	-2.022
observation->potCPUE->2003	-2.166	-2.166	-2.166	-2.166	-2.166	-2.166
observation->potCPUE->2004	-2.193	-2.193	-2.193	-2.193	-2.193	-2.193
observation->potCPUE->2005	-1.924	-1.926	-1.924	-1.924	-1.926	-1.924
observation->potCPUE->2006	-1.849	-1.852	-1.849	-1.849	-1.852	-1.849
observation->potCPUE->2007	-2.191	-2.191	-2.191	-2.191	-2.191	-2.191
observation->potCPUE->2008	-2.194	-2.194	-2.194	-2.194	-2.194	-2.194
observation->potCPUE->2009	-2.069	-2.070	-2.069	-2.069	-2.070	-2.069
observation->potCPUE->2010	-2.125	-2.127	-2.125	-2.125	-2.127	-2.125
observation->potCPUE->2011	-1.846	-1.837	-1.846	-1.846	-1.837	-1.846
observation->potCPUE->2012	-1.713	-1.702	-1.713	-1.713	-1.702	-1.713
observation->potCPUE->2013	-1.719	-1.713	-1.719	-1.719	-1.713	-1.719
observation->potCPUE->2014	-0.956	-0.954	-0.956	-0.956	-0.954	-0.956
observation->potCPUE->2015	-1.800	-1.800	-1.800	-1.800	-1.800	-1.800
observation->potCPUE->2016	-2.065	-2.066	-2.065	-2.065	-2.066	-2.065
observation->potCPUE->2017	-2.097	-2.098	-2.097	-2.097	-2.098	-2.097
observation->potCPUE->2018	-1.289	-1.285	-1.289	-1.289	-1.285	-1.289
observation->AFpotSurvey->2010	40.929	41.012	40.930	40.929	41.012	40.930
observation->AFpotSurvey->2014	39.709	39.711	39.709	39.709	39.711	39.709
observation->AFpotSurvey->2018	39.237	39.197	39.237	39.237	39.197	39.237
observation->AFpotFishing->2018	47.210	47.242	47.210	47.210	47.242	47.210
observation->AFpotFishing->2019	7.851	7.850	7.851	7.851	7.850	7.851
observation->lgobookLF	54.593	54.558	54.593	54.593	54.558	54.593
observation->rec.catch.LF	67.975	68.885	67.975	67.975	68.885	67.975
penalty->CatchMustBeTaken1	0.000	0.000	0.000	0.000	0.000	0.000
prior->B0->process[Recruitment].b0	9.586	9.586	9.586	9.586	9.586	9.586
prior->male_Linf->age_length[asMm0].linf	0.000	0.000	0.000	0.000	0.000	0.000
prior->male_cv2->age_length[asMm0].cv_last	0.000	0.000	0.000	0.000	0.000	0.000
prior->potSurvey_mA50->selectivity[potSurveySel_male].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->potSurvey_mAto95->selectivity[potSurveySel_male].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->potSurvey_fA50->selectivity[potSurveySel_female].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->potSurvey_fAto95->selectivity[potSurveySel_female].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->YCS->process[Recruitment].recruitment_multipliers{1983}	1.282	1.284	1.282	1.282	1.284	1.282
prior->YCS->process[Recruitment].recruitment_multipliers{1984}	1.313	1.315	1.313	1.313	1.315	1.313
prior->YCS->process[Recruitment].recruitment_multipliers{1985}	1.284	1.286	1.284	1.284	1.286	1.284
prior->YCS->process[Recruitment].recruitment_multipliers{1986}	1.153	1.155	1.153	1.153	1.155	1.153
prior->YCS->process[Recruitment].recruitment_multipliers{1987}	0.877	0.878	0.877	0.877	0.878	0.877
prior->YCS->process[Recruitment].recruitment_multipliers{1988}	0.435	0.435	0.435	0.435	0.435	0.435
prior->YCS->process[Recruitment].recruitment_multipliers{1989}	-0.054	-0.054	-0.054	-0.054	-0.054	-0.054
prior->YCS->process[Recruitment].recruitment_multipliers{1990}	-0.306	-0.306	-0.306	-0.306	-0.306	-0.306
prior->YCS->process[Recruitment].recruitment_multipliers{1991}	-0.081	-0.080	-0.081	-0.081	-0.080	-0.081
prior->YCS->process[Recruitment].recruitment_multipliers{1992}	0.761	0.764	0.761	0.761	0.764	0.761
prior->YCS->process[Recruitment].recruitment_multipliers{1993}	0.950	0.946	0.950	0.950	0.946	0.950
prior->YCS->process[Recruitment].recruitment_multipliers{1994}	0.058	0.057	0.058	0.058	0.057	0.058
prior->YCS->process[Recruitment].recruitment_multipliers{1995}	-0.167	-0.168	-0.167	-0.167	-0.168	-0.167
prior->YCS->process[Recruitment].recruitment_multipliers{1996}	-0.153	-0.152	-0.153	-0.153	-0.152	-0.153
prior->YCS->process[Recruitment].recruitment_multipliers{1997}	0.186	0.187	0.186	0.186	0.187	0.186
prior->YCS->process[Recruitment].recruitment_multipliers{1998}	0.900	0.898	0.899	0.900	0.898	0.899
prior->YCS->process[Recruitment].recruitment_multipliers{1999}	0.080	0.079	0.080	0.080	0.079	0.080
prior->YCS->process[Recruitment].recruitment_multipliers{2000}	-0.220	-0.220	-0.220	-0.220	-0.220	-0.220
prior->YCS->process[Recruitment].recruitment_multipliers{2001}	-0.197	-0.197	-0.197	-0.197	-0.197	-0.197
prior->YCS->process[Recruitment].recruitment_multipliers{2002}	-0.307	-0.307	-0.307	-0.307	-0.307	-0.307
prior->YCS->process[Recruitment].recruitment_multipliers{2003}	-0.202	-0.201	-0.202	-0.202	-0.201	-0.202
prior->YCS->process[Recruitment].recruitment_multipliers{2004}	-0.260	-0.260	-0.260	-0.260	-0.260	-0.260
prior->YCS->process[Recruitment].recruitment_multipliers{2005}	-0.137	-0.137	-0.137	-0.137	-0.137	-0.137
prior->YCS->process[Recruitment].recruitment_multipliers{2006}	0.087	0.083	0.087	0.087	0.083	0.087
prior->YCS->process[Recruitment].recruitment_multipliers{2007}	-0.131	-0.136	-0.131	-0.131	-0.136	-0.131
prior->YCS->process[Recruitment].recruitment_multipliers{2008}	0.118	0.126	0.118	0.118	0.126	0.118
prior->YCS->process[Recruitment].recruitment_multipliers{2009}	-0.089	-0.094	-0.089	-0.089	-0.094	-0.089
prior->YCS->process[Recruitment].recruitment_multipliers{2010}	-0.291	-0.285	-0.291	-0.291	-0.285	-0.291
prior->YCS->process[Recruitment].recruitment_multipliers{2011}	-0.187	-0.188	-0.187	-0.187	-0.188	-0.187
prior->YCS->process[Recruitment].recruitment_multipliers{2012}	-0.056	-0.055	-0.056	-0.056	-0.055	-0.056
prior->YCS->process[Recruitment].recruitment_multipliers{2013}	0.531	0.529	0.531	0.531	0.529	0.531
prior->YCS->process[Recruitment].recruitment_multipliers{2014}	-0.292	-0.291	-0.292	-0.292	-0.291	-0.292
prior->YCS->process[Recruitment].recruitment_multipliers{2015}	-0.254	-0.254	-0.254	-0.254	-0.254	-0.254
prior->YCS->process[Recruitment].recruitment_multipliers{2016}	-0.297	-0.297	-0.297	-0.297	-0.297	-0.297
prior->YCS->process[Recruitment].recruitment_multipliers{2017}	-0.128	-0.128	-0.128	-0.128	-0.128	-0.128
additional_prior->PrSurveyQ	-11.430	-11.430	-11.430	-11.430	-11.430	-11.430
additional_prior->PrCPUEQ	-8.366	-8.366	-8.366	-8.366	-8.366	-8.366
additional_prior->YCS_average_1	0.569	0.570	0.569	0.569	0.570	0.569
total_score	240.025	241.012	240.025	240.025	241.012	240.025

## [1] "CASAL base model convergence information"
## [1] "Minimiser convergence threshold: 2e-05"                                                                  
## [2] "Minimiser achieved convergence after 91 quasi-Newton iterations using 101 objective function evaluations"
## [1] ""
## [1] "CASAL sensitivity 1 model convergence information"
## [1] "Minimiser convergence threshold: 1e-07"                                                                   
## [2] "Minimiser achieved convergence after 100 quasi-Newton iterations using 119 objective function evaluations"
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model convergence information"
## [1] "fmm: have converged: t = 1.22737e-05 f = 240.025"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model convergence information"
## [1] "fmm: have converged: t = 7.44939e-06 f = 241.012"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model convergence information"
## [1] "fmm: have converged: t = 6.93126e-08 f = 240.025"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model convergence information"
## character(0)

## [1] "CASAL model warnings"
## NULL
## [1] ""
## [1] "CASAL sensitivity 1 model warnings"
## NULL
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model warnings"
## [1] "obs sum total (1.00001) for year (2010) doesn't sum to 1.0"                                                  
## [2] "obs sum total (0.99997) for year (2014) doesn't sum to 1.0"                                                  
## [3] "obs sum total (0.99998) for year (2018) doesn't sum to 1.0"                                                  
## [4] "obs sum total (1) for year (2018) doesn't sum to 1.0"                                                        
## [5] "obs sum total (1) for year (2019) doesn't sum to 1.0"                                                        
## [6] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model warnings"
## [1] "obs sum total (1.00001) for year (2010) doesn't sum to 1.0"                                                  
## [2] "obs sum total (0.99997) for year (2014) doesn't sum to 1.0"                                                  
## [3] "obs sum total (0.99998) for year (2018) doesn't sum to 1.0"                                                  
## [4] "obs sum total (1) for year (2018) doesn't sum to 1.0"                                                        
## [5] "obs sum total (1) for year (2019) doesn't sum to 1.0"                                                        
## [6] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model warnings"
## [1] "obs sum total (1.00001) for year (2010) doesn't sum to 1.0"                                                  
## [2] "obs sum total (0.99997) for year (2014) doesn't sum to 1.0"                                                  
## [3] "obs sum total (0.99998) for year (2018) doesn't sum to 1.0"                                                  
## [4] "obs sum total (1) for year (2018) doesn't sum to 1.0"                                                        
## [5] "obs sum total (1) for year (2019) doesn't sum to 1.0"                                                        
## [6] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model warnings"
## [1] "obs sum total (1.00001) for year (2010) doesn't sum to 1.0"                                                  
## [2] "obs sum total (0.99997) for year (2014) doesn't sum to 1.0"                                                  
## [3] "obs sum total (0.99998) for year (2018) doesn't sum to 1.0"                                                  
## [4] "obs sum total (1) for year (2018) doesn't sum to 1.0"                                                        
## [5] "obs sum total (1) for year (2019) doesn't sum to 1.0"                                                        
## [6] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model warnings"
## [1] "obs sum total (1.00001) for year (2010) doesn't sum to 1.0"                                                  
## [2] "obs sum total (0.99997) for year (2014) doesn't sum to 1.0"                                                  
## [3] "obs sum total (0.99998) for year (2018) doesn't sum to 1.0"                                                  
## [4] "obs sum total (1) for year (2018) doesn't sum to 1.0"                                                        
## [5] "obs sum total (1) for year (2019) doesn't sum to 1.0"                                                        
## [6] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model warnings"
## [1] "obs sum total (1.00001) for year (2010) doesn't sum to 1.0"                                                  
## [2] "obs sum total (0.99997) for year (2014) doesn't sum to 1.0"                                                  
## [3] "obs sum total (0.99998) for year (2018) doesn't sum to 1.0"                                                  
## [4] "obs sum total (1) for year (2018) doesn't sum to 1.0"                                                        
## [5] "obs sum total (1) for year (2019) doesn't sum to 1.0"                                                        
## [6] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"

1.5 Matching of outputs

Time series comparisons with CASAL base model results

## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Actual catches / Retained catch for line match: yes"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Actual catches / Retained catch for pot match: yes"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Actual catches / Retained catch for rec match: yes"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Actual catches / Retained catch for line match: yes"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Actual catches / Retained catch for pot match: yes"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Actual catches / Retained catch for rec match: yes"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Actual catches / Retained catch for line match: yes"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Actual catches / Retained catch for pot match: yes"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Actual catches / Retained catch for rec match: yes"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on"
## [1] "Actual catches / Retained catch for line match: yes"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Actual catches / Retained catch for pot match: yes"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Actual catches / Retained catch for rec match: yes"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_off"
## [1] "Actual catches / Retained catch for line match: yes"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Actual catches / Retained catch for pot match: yes"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Actual catches / Retained catch for rec match: yes"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on_low_tol"
## [1] "Actual catches / Retained catch for line match: yes"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Actual catches / Retained catch for pot match: yes"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Actual catches / Retained catch for rec match: yes"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""

Derived quantities

SB0, SBcurrent, MSY, F_MSY, others...

1.6 Plots

Comparison plots

## [1] "CASAL base parameter correlation range (excluding 1.0): -0.6876 0.9999"

## [1] "CASAL sensitivity 1 parameter correlation range (excluding 1.0): -0.6897 0.9999"

## [1] "Casal2 betadiff_casal_flags_on parameter correlation range (excluding 1.0): -0.660278 0.999651"

## [1] "Casal2 betadiff_casal_flags_off parameter correlation range (excluding 1.0): -0.714718 0.999691"

## [1] "Casal2 betadiff_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.715609 0.999626"

## [1] "Casal2 adolc_casal_flags_on parameter correlation range (excluding 1.0): -0.660277 0.999651"

## [1] "Casal2 adolc_casal_flags_off parameter correlation range (excluding 1.0): -0.714718 0.999691"

## [1] "Casal2 adolc_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.715609 0.999626"